Sandeep Kumar Rai

Postdoctoral Researcher • Boston Children’s Hospital & Harvard Medical School

I study how organized glycosaminoglycan landscapes at cellular interfaces — the cell surface, perineuronal nets, and the extracellular matrix — control the fate of molecules that cross them. My work bridges biomolecular condensate biophysics with extracellular matrix biology, using single-molecule and super-resolution tools to ask fundamental questions about neurodegenerative protein spreading and growth factor signaling.

Sandeep Kumar Rai

From a Village in India to Harvard

I grew up in Jaitpura, a small village in the Deoria district of Uttar Pradesh, India. My childhood was shaped by the rhythms of rural life — gilli-danda, cricket, pakadam-pakadaai, grazing cattle, working alongside family in the fields, and the kind of daily challenges that come with growing up in a place far remote from city, school, laboratories or universities. But that world taught me something no classroom could: how to observe carefully, how to be resourceful, and how to stay curious about why things work the way they do. The desire to understand — and the quiet determination to reach beyond what was immediately in front of me — is what eventually carried me out of the village and into science.

My early schooling happened at the school nearest to home, and my undergraduate studies in physics, chemistry, and mathematics were at Madan Mohan Malviya PG College in nearby town, Bhatpar Rani. Science, at that stage, was still textbooks and exams — I hadn’t yet seen what research actually looked like. That changed when I moved to IIT Delhi for my Master’s in Chemistry. For the first time, I stepped into a real research laboratory, saw how scientific questions get asked and answered, and encountered the world of interdisciplinary science. The distance between a farming village in eastern UP and a research lab in Delhi felt enormous — but crossing it only sharpened my appetite for asking bigger questions.

That conviction led me to the Indian Institute of Science Education and Research (IISER) Mohali for my PhD, where I joined Prof. Samrat Mukhopadhyay’s lab. Here, I discovered the world of biomolecular condensates — dynamic, liquid-like assemblies of proteins and RNA that organize cellular life but, when they go wrong, drive devastating neurodegenerative diseases. Using single-molecule FRET, super-resolution microscopy, and Raman spectroscopy, I dissected how tau, prion protein, and α-synuclein commingle into pathological co-aggregates and how molecular chaperones can arrest these transitions. That work resulted in first-author papers in PNAS and Science Advances.

By the end of my PhD, I knew what I wanted next: to understand the biology of the cell surface, where organized molecular assemblies mediate everything from signaling to immune recognition. In 2024, I moved to Boston Children’s Hospital and Harvard Medical School to join Ryan Flynn’s lab, where I’m now studying cell-surface RNA biology, membrane organization, and the emerging landscape of glycosaminoglycan-mediated signaling. This training has given me a second intellectual home — in glycobiology, membrane biology, and chemical biology — that I now integrate with my biophysics roots.

The thread running through everything: from grazing cattle in a village in eastern Uttar Pradesh, through biomolecular condensates in Mohali, to cell-surface organization in Boston — at each step, I’ve been drawn to the same kind of problem: how do disordered molecules organize themselves into something functional, and what goes wrong when they don’t?

“An individual is only as good as their surroundings — so thanks to all of them.”

🌍 View my journey on the map →

Current & Doctoral Work

CURRENT — FLYNN LAB, BOSTON CHILDREN’S HOSPITAL

Cell-Surface RBP–HSPG Clusters & Membrane Organization

Characterizing how RNA-binding proteins, heparan sulfate proteoglycans, and glycoconjugates form organized nanoclusters on the cell surface, and how these clusters orchestrate membrane organization and integrity.

GAG Phase Separation & Polymer Physics

Investigating whether glycosaminoglycans can act as condensate scaffolds through their sticker-spacer architecture, with implications for how the cell-surface landscape self-organizes.

DOCTORAL WORK — THE MUKHOPADHYAY LAB, IISER MOHALI

Heterotypic Condensates & Co-aggregation

Demonstrated that tau and prion protein undergo complex coacervation via domain-specific electrostatic interactions, forming multiphasic condensates that convert into heterotypic amyloid co-aggregates — hallmarks of overlapping neurodegenerative diseases.

Chaperone-Mediated Regulation

Uncovered how the molecular chaperone Hsp40 (Ydj1) promotes heterotypic phase separation of tau and arrests pathological liquid-to-solid transitions at an intermediate state, revealing a protective mechanism.

Single-Molecule Conformational Biology

Applied single-molecule FRET to probe polypeptide conformational distributions within condensed phases at single-molecule resolution, revealing structural subpopulations and critical molecular events during phase separation.

Water & Hydration Dynamics in Condensates

Used label-free vibrational Raman spectroscopy to observe sequence-dependent reorganization of hydrogen-bonding networks upon phase separation — within condensates and in the surrounding dispersed phase.

Toward an Independent Research Program

“How does the physical state and sulfation chemistry of glycosaminoglycan landscapes at cellular interfaces — the cell surface, the perineuronal net, the extracellular matrix — gate the spreading of neurodegenerative protein seeds and the access of growth factors to neurons?”

🧬

GAG-Mediated Gating of Prion-like Protein Spreading

Do perineuronal nets protect neurons from tau pathology or paradoxically catalyze it? Reconstituting minimal PNNs with defined CS composition to measure tau seed conformation, penetration kinetics, and fibril conversion at single-molecule resolution.

smFRETSingle-particle trackingReconstituted PNNs
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Perineuronal Nets as Selective Growth Factor Filters

PNNs aren’t uniform barriers — they selectively gate different growth factors based on CS sulfation patterns, reshaping the signaling landscape around PNN-enwrapped neurons.

SPR/BLIPrimary neuronsTIRF
⚛️

GAG Phase Separation & Polymer Physics

Characterizing homotypic HS and CS phase separation with divalent cations, testing whether the cell-surface GAG landscape is a pre-organized condensate platform.

FRAPPhase diagramsPolymer theory
🏗️

Cell-Surface Membrane Organization

Understanding how GPI-anchored proteins, syndecans, and glypicans create organized signaling nanodomains and how disease rewires this architecture.

Super-resolutionChemical biologyLive-cell imaging

Peer-Reviewed Work

bioRxiv (Preprint) • 2025

Catch and release of sialoglycoRNAs enables sequencing-based profiling across cellular and extracellular material

Ge, R., Jeppesen, D. K., Rai, S. K., Zhang, Q., Higginbotham, J. N., Coffey, R. J., & Flynn, R. A.

Nature • 2026

GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling

Chai, P., Kheiri, S., Kuo, A., Shah, J., Kageler, L., Ge, R., Perr, J., Porat, J., Lebedenko, C. G., Dias, J. M. L., Yankova, E., Rai, S. K., Watkins, C. P., Hristov, P., Tzelepis, K., Hla, T., Raman, R., Calo, E., Esko, J. D., & Flynn, R. A.

Science Advances • 2025

Chaperone-mediated heterotypic phase separation regulates liquid-to-solid phase transitions of tau into amyloid fibrils

Rai, S. K., Khanna, R., Sarbahi, A., Joshi, A., & Mukhopadhyay, S.

First Author DOI →

PNAS • 2023

Heterotypic electrostatic interactions control complex phase separation of tau and prion into multiphasic condensates and co-aggregates

Rai, S. K., Khanna, R., Avni, A., & Mukhopadhyay, S.

First Author DOI →

Nature Communications • 2022

Spatiotemporal modulations in heterotypic condensates of prion and α-synuclein control phase transitions and amyloid conversion

Agarwal, A., Arora, L., Rai, S. K., Avni, A., & Mukhopadhyay, S.

PNAS • 2021

An intrinsically disordered pathological prion variant Y145Stop converts into self-seeding amyloids via liquid-liquid phase separation

Agarwal, A.§, Rai, S. K.§, Avni, A., & Mukhopadhyay, S.

Co-First Author DOI →

Nature Communications • 2023

Single-molecule FRET unmasks structural subpopulations and crucial molecular events during FUS low-complexity domain phase separation

Joshi, A., Walimbe, A., Avni, A., Rai, S. K., Arora, L., Sarkar, S., & Mukhopadhyay, S.

J. Phys. Chem. Lett. • 2024

Hydrogen-bonded network of water in phase-separated biomolecular condensates

Joshi, A., Avni, A., Walimbe, A., Rai, S. K., Sarkar, S., & Mukhopadhyay, S.

Protein Science • 2021 — Review

Liquid-liquid phase separation of tau: From molecular biophysics to physiology and disease

Rai, S. K., Savastano, A., Singh, P., Mukhopadhyay, S., & Zweckstetter, M.

Review DOI →

View all publications on Google Scholar →

Education & Positions

2024 – Present

Postdoctoral Researcher

Boston Children’s Hospital — Ryan Flynn Lab

Cell-surface RBP–HSPG clusters, membrane organization, chemical biology & glycobiology

2018 – 2024

Ph.D. in Molecular Biophysics

IISER Mohali, India — Samrat Mukhopadhyay Lab

Biomolecular condensates, IDP phase separation & neurodegeneration

2016 – 2018

M.Sc. in Chemistry

Indian Institute of Technology (IIT) Delhi

Master’s thesis with Prof. Shashank Deep

2012 – 2015

B.Sc. in Physics, Chemistry & Mathematics

Madan Mohan Malviya PG College, Bhatpar Rani (affiliated with DDU Gorakhpur University)

Honors

National PhD Fellowship — Council of Scientific and Industrial Research (CSIR), Government of India • All India Rank 74

Methods & Approaches

Single-Molecule & Imaging

Chemical Biology & Biophysics

Contact

Email

sandeepkumar.rai [AT] childrens.harvard.edu
rai501951 [AT] gmail.com

Institution

Boston Children’s Hospital
Stem Cell Program
Ryan Flynn Lab

eRA Commons

SANRAI

Open to collaborations & academic discussions